I know there have been a lot of Ideas regarding the Block Diagram Cleanup tool, but I haven't seen this one suggested.
There should be an option to force Block Diagram Cleanup (CTRL-U) to only act on wires. Essentially it would be the same as selecting all wires, right-clicking and selecting Clean Up Wire.
Similar Ideas, but not the same:
http://forums.ni.com/t5/LabVIEW-Idea-Exchange/Clean-Up-Wire-function-for-several-wires/idi-p/1213463
I'm almost certain that there is a scripting method available to accomplish this.
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